Delineating genetic relationships among the Maya

The Analysis of Autosomal STRs Draws the Current Genetic Map and Evolutionary History of Northernmost South America

OBJECTIVES

To analyze Colombia's current human population, we employed a population genetics approach enriched by genealogical, demographic, cultural, and historical data to learn about its evolutionary history and to elucidate ethnic belonging and relationship patterns between its various population groups.

MATERIALS AND METHODS

This study relied on ten autosomal microsatellite markers (STRs) from 1364 individuals surveyed throughout the country. Aside from employing descriptive population genetics, substructure, and distance analysis, this investigation evaluated genealogical, demographic, cultural, and historical data gathered from fieldwork surveys.

RESULTS

We present a genetic diversity and ethnic belonging map of Colombia that suggests a nine-population classification (under Afro-descendant, Native American, and Admixed ethnicity labels) that reveals traces of evolutionary processes discussed in the light of the recent literature based on modern molecular markers. Colombia's genetic trace from Africa varies among territories, as shown here by two differentiated Afro ancestral components, Chocó and San Andrés, in addition to the Afro admixture category. Some Native American peoples like the Wayúu, Zenú, Ticuna, Huitoto, and Cocama have a genetic configuration that remains relatively preserved. Nevertheless, other self-determined indigenous peoples who remain in their ancestral territories exhibit genetic introgression that is also reflected by their acculturation levels such as the Pijaos, Kankuamos, and Mokaná. The population classified as European admixture also shows an ancestral component that seems to be more fixed throughout neighboring territories but whose fluctuation depends on its specific demographic histories.

CONCLUSIONS

This study combines STRs, a targeted sampling strategy, and advanced analytical tools to explore Colombia's genetic diversity and evolutionary history. Locally, these findings enhance the understanding of genetics in a post-conflict society, crucial for human identification. Globally, they contribute to human population genetics, helping address evolutionary questions using data from diverse human ancestries and geographies.

Genetic diversity, structure, and admixture in Mayans from Guatemala and Mexico based on 15 short tandem repeats

OBJECTIVE

To analyze the genetic origin, relationships, structure, and admixture in Mayan Native American groups from Guatemala and Mexico based on 15 autosomal short tandem repeats (STRs) loci commonly used in human identification (HID).

METHODS

We genotyped 513 unrelated Mayan samples from Guatemala based on 15 STR loci (AmpFlSTR® Identifiler kit). Moreover, we included 4408 genotypes previously reported, as following: Mayas from Guatemala and Mexico (n = 1666) and from Latin American, European, and African (n = 2742) populations. Forensic parameters, genetic distances, admixture, and population structure were assessed.

RESULTS

Forensic parameters of the 15 STRs in different Mayan groups from Guatemala were reported. Low (Fst = 0.78%; p = 0.000) and non-significant differentiation (Fst = 1.8%; p = 0.108) were observed in Mayas from Guatemala and Mexico, respectively. The relative homogeneity observed among Mayan groups supported theories of extensive pre-Columbian gene flow and trade throughout the Mayan Empire. The distribution of the three Native American ancestries among these Mayan groups did not support the presumable Guatemalan origin of Tojolabal and Lacandon people (South, Mexico). The nonsignificant differentiation between Ladinos and Mayas suggests a relative panmixia in Guatemala. Mestizos from southeastern Mexico and Guatemala constitute a core of Native American ancestry in Latin America related to the Mayan Empire in Central America.

CONCLUSIONS

The higher European admixture and homogeneity in Mexican Mayas of the Yucatan Peninsula suggest more intensive post-Columbian gene flow in this region than in Guatemalan Mayas.

Mayans: a Y chromosome perspective

In spite of the wealth of available cultural and archeological information as well as general interest in the Mayans, little is known about their genetics. In this study, for the first time, we attempt to alleviate this lacuna of knowledge by comprehensively investigating the Y chromosome composition of contemporary Mayan populations throughout their domain. To accomplish this, five geographically targeted and ethnically distinct Mayan populations are investigated using Y-SNP and Y-STR markers.

FINDINGS

overall, the Mayan populations as a group are highly homogeneous, basically made up of only two autochthonous haplogroups, Q1a2a1a1*-M3 and Q1a2a1*-L54. Although the Y-STR data illustrates diversity, this diversity, for the most part, is uniformly distributed among geographically distant Mayan populations. Similar haplotypes among populations, abundance of singletons and absence of population partitioning within networks among Mayan populations suggest recent population expansion and substantial gene flow within the Mayan dominion, possibly due to the development of agriculture, the establishment of interacting City-State systems and commerce.

Importance of the geographic barriers to promote gene drift and avoid pre- and post-Columbian gene flow in Mexican native groups: Evidence from forensic STR Loci

OBJECTIVE

To analyze the origin, structure, relationships, and recent admixture in Mexican Native groups based on 15 STRs commonly used in human identification.

METHODS

We analyzed 39 Mexican Native population samples using STR databases based on the AmpFlSTR® Identifiler kit (n = 3,135), including Mexican-Mestizos (admixed), European and African populations, as reference.

RESULTS

Based upon effective population size (Ne) differences, Native groups were clustered into three regions: i) Center-Southeast groups, characterized by larger Ne, migration rate (Nm), genetic diversity (He), and relative homogeneity principally in the Yucatan Peninsula; ii) Isolated southern groups from Chiapas and Oaxaca, characterized by lower Ne, Nm, and He (i.e. higher isolation and genetic differentiation); iii) North-Northwest groups, which are similar to the previous group but are characterized by generating the widest gene flow barrier in the Pre-Hispanic Mexican territory, and currently by elevated admixture in some northern Native groups. Despite the relative congruence between genetic relationships with cultural, linguistic, geographic criteria, these factors do not explain the present-day population structure of Native groups, excepting in those linguistically related to the Mayan that show higher homogeneity. The Isolation by distance model was demonstrated at long distances (>1,500 km), whereas geographic isolation stands as a determining factor to avoid both non-indigenous admixture and bottleneck processes.

CONCLUSIONS

Different dynamics of gene flow and drift were observed among Mexican Native groups, highlighting the geographic barriers (mountains, canyons and jungle regions) as the main factor differentiating Pre-Hispanic populations, and eventually helping to avoid Post-European contact admixture and population bottleneck. Am J Phys Anthropol 160:298-316, 2016. © 2016 Wiley Periodicals, Inc.

A Mayan founder mutation is a common cause of deafness in Guatemala

Over 5% of the world's population has varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (ARNHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a ARNHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared with those of Native American, European, and African populations shows a close match with the Mayan population.

Genomic insights on the ethno-history of the Maya and the 'Ladinos' from Guatemala

Background

Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs).

Results

Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America.

Conclusions

The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.

United Arab Emirates: phylogenetic relationships and ancestral populations

In the current report, 109 unrelated individuals from the United Arab Emirates (UAE) were typed across 15 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D149S433, vWA, TPOX, D18S51, D5S818 and FGA) routinely employed in population genetics analyses and compared across a set of ethnically and geographically targeted reference collections. UAE, located at the southeastern most portion of the Arabian Peninsula, in the tri-continental crossroads connecting Africa, Europe and Asia, has been influenced by a number of human dispersal waves from a plethora of sources including the Paleolithic "Out of Africa" migrations, the exodus of Neolithic pastoral agriculturalists from the Fertile Crescent and Northern Africa, as well as more recent migrations from Asia and the Middle East. We found that despite the high levels of consanguinity that characterize UAE, this population is genetically highly heterogeneous. When compared to various world-wide biogeographical regions, the Arabian Peninsula exhibits the highest intra-population variance. Admixture analyses indicate that UAE and Bahrain uniquely in Arabia share 23.7% and 22.9%, respectively, of their DNA with Southwest Asian populations. Similar and complex Structure profiles are seen among Arabian Peninsula populations underscoring the high genetic diversity of the region. Although UAE shares a number of genetic characteristics in common with the rest of the populations in the Arabian Peninsula, it is unique in terms of its relative high Asian genetic component, likely the result of geographical proximity to Southwest Asia, west-bound waves of migration and socio-political ties with territories to the east.

Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups

The maternal ancestry (mtDNA) has important applications in different research fields, such as evolution, epidemiology, identification, and human population history. This is particularly interesting in Mestizos, which constitute the main population in Mexico (∼93%) resulting from post-Columbian admixture between Spaniards, Amerindians, and African slaves, principally. Consequently, we conducted minisequencing analysis (SNaPshot) of 11 mitochondrial single-nucleotide polymorphisms in 742 Mestizos of 10 populations from different regions in Mexico. The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively). Conversely, European and African ancestries were less frequent (5.3 and 1.9%, respectively). The main characteristics of the maternal lineages observed in Mexican-Mestizos comprised the following: 1) contrasting geographic gradient of Haplogroups A and C; 2) increase of European lineages toward the Northwest; 3) low or absent, but homogeneous, African ancestry throughout the Mexican territory; 4) maternal lineages in Mestizos roughly represent the genetic makeup of the surrounding Amerindian groups, particularly toward the Southeast, but not in the North and West; 5) continuity over time of the geographic distribution of Amerindian lineages in Mayas; and 6) low but significant maternal population structure (FST  = 2.8%; P = 0.0000). The average ancestry obtained from uniparental systems (mtDNA and Y-chromosome) in Mexican-Mestizos was correlated with previous ancestry estimates based on autosomal systems (genome-wide single-nucleotide polymorphisms and short tandem repeats). Finally, the comparison of paternal and maternal lineages provided additional information concerning the gender bias admixture, mating patterns, and population structure in Mestizos throughout the Mexican territory.

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.

On the origins, rapid expansion and genetic diversity of Native Americans from hunting-gatherers to agriculturalists

Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.

Analyzing the genetic structure of the Tepehua in relation to other neighbouring Mesoamerican populations. A study based on allele frequencies of STR markers

We report data on the genetic variation of the Tepehua population based on 15 autosomal microsatellites. The Tepehua, whose language belongs to the Totonac family, are settled throughout the Sierra Madre Oriental in Mexico and constitute a group in demographic decline. The results suggest that the Tepehua population remained isolated throughout a large part of its history. Phylogenetic analyses performed with other indigenous and admixed populations of Mesoamerica allow us to address their biological history. The results suggest a genetic affinity between the Tepehua and the Huastecos due to their previous shared history, and a certain degree of differentiation from the Otomões groups and the Choles (who are of Mayan origin). A clear genetic differentiation is also apparent between native and admixed populations within the greater region of Mesoamerica. It is currently accepted that the genetic composition of the American populations fits a trihybrid model of admixture. The genetic structure based on comparison of 34 populations throughout the continent (9 indigenous and 23 admixed) using hierarchical cluster analysis with an explained variance of 61.17% suggests the existence of four large groups distinguished according to the degree of admixture between Amerindians, Europeans, and Africans.

The genetic legacy of the Transatlantic Slave Trade in the island of New Providence

The Bahamian archipelago has been influenced by a wide array of settlers (Lucayans, Eleutherian Adventurers, British Loyalists, Creoles from the United States and African slaves) throughout its short but dynamic history. Nevertheless, the Bahamas remains poorly characterized genetically and little is known about each group's contribution to the island chain. In the current study, the population of New Providence was analyzed based on 15 autosomal STR loci routinely employed in forensic DNA fingerprinting applications. A comparison of this collection with African groups reveals similar genetic profiles to West African populations from Equatorial Guinea and Angola, possibly resulting from the importation of slaves from West African ports during the Transatlantic Slave Trade. Although the New Providence collection exhibits strong genetic affinities to the two US African American reference populations, the detection of unique alleles among them may necessitate the utilization of population-specific databases in forensic cases especially when the STR profiles include these specific variants.